The quantification of traces of chimeric cell-free DNA (cfDNA), i.e., (cfDNA that comprises normal genomic DNA from a patient and DNA from another individual or DNA from patient tissue or cells that differ from normal genomic DNA) is useful as a diagnostic maker in cancer, solid organ transplantation and fetal aneuploidy. However, compared to other established biochemical tests, standardization suffers from obstacles, such as low concentrations and fragmentation of cfDNA. Digital PCR enables a high precision in quantification, but thorough error control is needed for reliable measurements. This invention addresses the need for improved quantification for digital PCR methods that assess chimeric cf DNA.